1. The official version number of the developer
2. The version number of the installer setup file
3. The mysterious gog-xx version number

That is VERY confusing!

waaayy too much freetime

1 refers to the game's version, while 2 refers to the installer's version. Why keep a version for the installer different than the game's version? Because GOG can update a game's installer for various things (like add more languages or issue GOG-specific fixes) without changing the game's version itself.

3 is the same as 2. Specifically, the xx part of gog-xx refers to the last two digits of the installer's number as a quick way to check whether you have the latest installer. For instance, 7th Guest has version number gog-17 and the installer's version number is 2.0.0.17.

Could it be done better? Sure it could, but that could be said for quite a few things here on GOG.

For example: The current version of 80-days is 1.11g but the installer for this version is 80_days_2.3.0.5. The numbers not match.

Poles are highly intelligent. They need things like that to keep them busy or else they start playing a game that combines drinking and chess...

And they never will. As Gragar explained, the installer can be updated to include features and fixes that do not change the game version, hence the two different version numbers.

Which ends up looking like this